Species in Phytozome v9.1

Welcome to Phytozome!

Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of release v9.1, Phytozome provides access to forty-one sequenced and annotated green plant genomes which have been clustered into gene families at 20 evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable.

[30 Jan 2015]
System Maintenance Feb 3-4 2015.
The next NERSC "quarterly maintenance" will take place beginning Tuesday, February 3, 07:00 PST, and ending Wednesday, February 4, 12:00 PST (noon). As many of you are already aware, NERSC provides all Phytozome-related computational resources, including our web presence.

This is a longer maintenance period than usual, and could impact Phytozome system stability and availability from early Tuesday morning until Wednesday at noon (that is a worst case scenario). We know in particular that all NERSC dependent systems, including Phytozome, will be completely unavailable between 8:00 am and 10:30 am Tuesday.

[19 Jun 2014]
Phytozome v9 bulk data access moved to JGI Genome Portal.
As we continue to move Phytozome v9 towards retirement, we have transferred bulk data access capabilities from the Phytozome FTP site to the JGI Genome Portal, which provides fast, authenticated access to all public JGI data. In keeping with the JGI's requirement that only registered users can access JGI data, we have disabled access to the FTP site from Phytozome v9 organism pages, species menus, and the search interface. Each organism page now contains a link to the corresponding organism page in Phytozome v10. Those wishing to access v9 organism data sets can find them at the JGI Genome Portal for Phytozome v9.

[24 Jan 2014] Updates and early releases: Soybean, Panicum hallii, Brassica rapa FPsc now available.As users await the full release of v10 of Phytozome, expected in the next few weeks, we have decided to make available 3 updated projects: the re-assembly (a2) and re-annotation (v1) of Glycine max, the v1.3 assembly and annotation of Brassica rapa FPsc, and a preliminary annotation and assembly of Hall's panicgrass, Panicum hallii. Gene pages, genome browsers, and data access via BioMart are available for all 3 genomes.

[30 Sep 2013] Early release of Panicum virgatum v1.1 annotationBased on a new v1.0 assembly, the new v1.1 early release annotation of switchgrass (Pancium virgatum) is now available.